1. Field of the Invention
The present invention generally relates to the field of biocontrol of disease in animal production systems and more specifically to a method, system and computer program product for the technical management and biocontrol of disease in animal production systems by use of microbial biotechnology. The present invention includes use of various technologies described in the references identified in the appended LIST OF REFERENCES and/or cross-referenced throughout the specification by numerals in brackets corresponding to the respective references, the entire contents of all of which are incorporated herein by reference.
2. Discussion of the Background
Aquatic farming is the fastest growing sector of international agribusiness today (estimated farm gate value over US$30 billion/yr), with double-digit growth in major geographic regions where fish and shrimp are grown commercially. Sustained growth in aquaculture is needed to compensate for declining traditional fisheries and to meet a growing demand for high-value protein. Harvests of marine and freshwater finfish and shellfish for human consumption (herein defined as seafood) from the world's capture fisheries has been relatively stagnant at about 60 million tonne/yr over the last several years. During this time, major commercial fishing grounds have been classified as “Fully Exploited” or “Over Exploited.” The Food and Agriculture Association (FAO) estimates world annual demand for seafood in the year 2010 at 110 to 120 million tonne. Best-case projections show a world supply of about 114 million tonne with less-favorable estimates at about 74 million tonne. A realistic scenario shows a deficit of 36 million to 46 million tonne. [1] Based on FAO and other estimates, about 10 million tonne of aquafeed will be used in the world in 1999 to feed the cultured of fish and shrimp.
At the same time, all segments of the aquaculture industry, e.g., shrimp, finfish, shellfish, etc., are being strongly affected by disease, especially bacterial diseases. Farmed shrimp production, which reached 737,200 tonne live weight in 1998 with an estimated trade value of about US$6 billion, is the most valuable export aquaculture crop and the hardest hit by disease in terms of financial losses to the industry. About 80% of the world's shrimp production takes place in Asia, the rest predominantly in Latin America. Thailand has been the world's largest farmed shrimp producer with over 210 000 tonne/yr and Ecuador was second with over 130,000 tonne; the production in both countries have been significantly affected by disease.
The damage caused by bacterial and viral diseases to the shrimp industry has been in the billions of dollars. Pathogenic Vibrio bacteria and viruses, such as Yellow Head Virus, White Spot (WSV) and Taura Virus have been among the most damaging pathogens. Central America was hit hard in 1999 by WSV and pathogenic Vibrio disease, causing great losses in production, for example, up to 50% in some countries. WSV can result in 100% mortality within the first few weeks after stocking shrimp ponds. Ecuador, the largest shrimp producing country in the Western Hemisphere was severely affected by WSV in 1999 and is estimated to have lost more than 40% of its annual production with no signs of significant recovery to date.
Chemicals and heavy use of antibiotics are the most commonly used methods to control shrimp diseases. However, these processes can be ineffective and dangerous. Indiscriminate use of antibiotics and disinfectants has led to an increase in bacteria having multiple antibiotic resistances. Many of the pathogens appear to have mutated to more virulent forms than were present a decade ago, resulting in greater rates of shrimp mortality. Thus, the incidence of the disease has been exacerbated by the actions of the shrimp farmers themselves using antibiotics.
Use of most chemicals and drugs is prohibited in the United States shrimp farming, wherein shrimp imports are tested for chemical residues and U.S. authorities have rejected shipments. Furthermore, the concern of potential transfer of antibiotic resistance to human pathogens and the negative marketing image created by use of chemicals and drugs can slow the growth and damage the aquaculture industry in the long-term.
The major disease agents around the world in aquaculture are bacteria, especially Vibrio species in marine systems. Often, a combination of viral and bacterial disease appears to be a widespread cause of mortality. For example, shrimp exposed to heavy environmental stress can be severely weakened by Vibrio sp. favoring invasion and increasing pathogenicity by virus, such as WSV. Conversely, shrimp that are infected by virus, but normally tolerate its pathogenicity can succumb to the virus with the additional stress of Vibrio infection.
Currently, pharmaceutical companies sell antibiotics to aquatic farmers. In addition, it is quite likely that problems have been exacerbated by the use of other antimicrobial compounds. Chlorine is widely used in hatcheries and ponds, but its use stimulates the development of multiple antibiotic resistance genes in bacteria [28, 29]. If antibiotics are used to kill bacteria, there are always some bacteria that survive, either strains of the pathogen or others, because they carry genes for resistance. These will then grow rapidly because their competitors are removed. Virulent pathogens that then re-enter the tank, perhaps from within biofilms in water pipes or in the guts of animals, can then exchange genetic information with the resistant bacteria and survive further doses of antibiotic. Thus, antibiotic-resistant strains of pathogens evolve rapidly [35].
The transfer of resistance to human pathogens and gut bacteria is of major concern. Such transfers probably happen easily and often. A gene coding for tetracycline resistance has been transferred between Prevotella, bacteria that normally live in the rumen of farm animals, and Bacteriodes, bacteria that normally live in human guts [30]. Resistance plasmids (R plasmids) encoding for many antibiotic resistance genes were transferred between pathogenic and non-pathogenic Gram negative bacteria in several environments including sea water [31]. In the presence of tetracycline concentrations that were not high enough to kill the bacteria, the rate of gene transfer between Vibrio cholerae and Aeromonas salmonicida increased 100 times.
This work raises questions not only about the use of antibiotics in aquaculture, but about the use of bacteria closely related to pathogenic species as probiotics. Not only antimicrobial resistance genes, but also genes for virulence can be transferred by R plasmids and transposons [32]. As the R plasmids can transfer genes between widely different bacteria in the Gram negative group, it would be potentially dangerous to use Vibrio or Pseudomonas, for example, as probiotics. However, the use of such bacteria is promoted, particularly Vibrio alginolyticus [33]. Based on observations by the present inventors, it is noted that the efficacy of Vibrio species as probiotics is short lived. Indeed, strains of Vibrio alginolyticus have been reported as virulent pathogens of shrimp larvae [34].
Throughout Asia, prawn farmers use antibiotics in large quantities. Warehouses supplying the industry in all the major centers sell a range of antibiotics in containers of 500 g or more in size. The antibiotics in current use include fluoroquinolones especially norfloxacin and enrofloxacin, furazolidone, oxolinic acid, oxytetracycline, trimethoprim and sulphadiazine. It is difficult to find out just how much antibiotic use there is in the industry, but it is possible to make an estimate from feed usage and production. In 1994, Thailand produced about 250,000 tonnes (a quarter of the world production) of farmed prawns, which consumed about 500,000-600,000 tonnes of feed. With the disease problems, prawn production has dropped to as low as 150,000 tonnes. For each crop at semi-intensive to intensive scales of production, farmers use 5-10 g antibiotics per kg feed at least once per day at weekly intervals; some use them for more extensive periods. Thus, as antibiotics would be used in about 10% of feed, the antibiotic usage in prawn farm production Thailand alone would be about 300-600 tonnes per year. And this does not include that used in hatcheries for fry production. As much of this will end up producing bacteria with multiple antibiotic resistance in farm effluents that then contaminate coastal waters, the potential impact on human health is significant [32, 35].
The overall strengths of antibiotics in the market place are long-term conditioning of individuals to the value of antibiotics for human and animal therapy; strong and well-financed marketing, and immediate short-term benefit. In most cases, the farmer does not see the long-term resistance build up and increased virulence until too late. Although some aquaculture producers are now realizing that they must move away from antibiotics, there are many who still use antibiotics. Antibiotics are recognized for their serious contribution to the collapse or decline of the shrimp industries in Taiwan, China, India, Thailand, and Philippines.
The use of probiotics to fight disease can be much more effective than use of antibiotics. The term “probiotic” was coined in the 1970s as a contrast to antibiotic and refers to beneficial bacteria found in the stomachs and intestines of animals that aid the animal in digestion and in fighting hazardous, disease-causing bacteria That is, when beneficial bacteria that are normal internal residents of the animal are added in larger numbers than present naturally, they promote health of the animal, in other words, they help the animal fight disease organisms. The probiotic approach to fighting disease does not share the above-noted disadvantages of an antibiotic approach. However, simply adding beneficial bacteria to aquaculture systems typically does not necessarily provide a solution to disease.
Among the companies attempting to combat disease in aquaculture are fermentation companies that manufacture or sell microbial products for industries other than aquaculture. However, fermentation companies and/or their marketers typically do not understand aquatic microbial ecology and aquaculture. These companies typically sell products that are inappropriate, ineffective and/or too expensive for aquatic farmers.
There are several dozen companies around the world selling bacteria referred to as “probiotics,” although in most cases, the bacteria they sell do not meet the definition or function of probiotics, and indeed some are pathogens. Many companies are now selling Lactobacillus bacteria for fighting disease in shrimp aquaculture, but Lactobacillus is a probiotic for terrestrial animals and is the wrong bacterium for seawater and crustaceans. In many cases the microbial products may be suitable for wastewater treatment and bioremediation, but are not appropriate for disease control in aquaculture i.e., the bacteria do not have the genetic or molecular capacity to prevent disease. Most commercial products have very low concentrations of bacteria making them ineffective when added to large water volumes in aquaculture containment systems such as grow-out ponds. Some commercial companies have attempted to overcome the problem of low bacterial concentrations by requiring on-site fermentation by customers to generate sufficient numbers of bacteria to add to the large quantities of water in aquaculture containment systems.
An exemplary background art system of FIG. 10 includes a technology deployer 1002, a manufacturer 1004, a distributor 1006 and end users 1008 to 1010. In FIG. 10, the technology deployer 1002 determines bacteria 1038 that are perceived to have beneficial properties based presumably on scientific literature or based on their experience and on their ability to manufacture 1004 the bacteria 1038 in low concentration form by commercial fermentation methods. The distributor 1006, and /or the manufacturer 1004 in the case where sales are direct, then sells these bacteria 1038 to the end users 1008 to 1010. The more advanced technology deployers may perform bioassays in their labs to test the ability of their bacterial strains, which they are able to produce commercially, to inhibit generic pathogens, but typically do not test against strains selected from individual end user 1008 to 1010 locations. In some cases, the product 1038 must be further fermented in media by the end users 1008 to 1010 to increase the number of microbes before application at the end user 1008 to 1010 locations.
The above solutions are not effective in disease prevention and do not offer biocontrol of disease in aquaculture systems due to: (i) poor understanding of the physical, chemical and biological factors that affect disease control in commercial aquaculture systems, (ii) lack of technical support at the end user location (iii) lack of management of information generated by end user and its timely linkage to deployment of an appropriate technological response to epizootic conditions (iv) microbial products that do not prevent disease in commercial aquaculture systems, (v) microbial products that are not cost effective, and (vi) microbial products that are not user-friendly.